Mercurial > repos > davidvanzessen > argalaxy_tools
diff imgt_loader/imgt_loader.r @ 46:4d2a8f98a502 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 28 Jan 2019 09:37:41 -0500 |
| parents | 106275b54470 |
| children | 124b7fd92a3e |
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--- a/imgt_loader/imgt_loader.r Fri Dec 08 06:32:16 2017 -0500 +++ b/imgt_loader/imgt_loader.r Mon Jan 28 09:37:41 2019 -0500 @@ -33,6 +33,16 @@ return(df) } +print_missing_columns = function(df, cols, label=""){ + cols_in_df = cols %in% names(df) + if(sum(!cols_in_df) > 0){ + print("Columns are missing from summary file, don't have:") + print(cols[!cols_in_df]) + } else { + print(paste("No missing columns for", label)) + } +} + summ = fix_column_names(summ) sequences = fix_column_names(sequences) aa = fix_column_names(aa) @@ -51,7 +61,9 @@ added_junction_columns=c('P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION') added_junction_columns=c(added_junction_columns, 'P5.D1.nt.nb', 'P3.D1.nt.nb', 'N2.REGION.nt.nb', 'P5.D2.nt.nb', 'P3.D2.nt.nb', 'N3.REGION.nt.nb', 'P5.D3.nt.nb', 'P3.D2.nt.nb', 'N4.REGION.nt.nb', 'X5.D1.REGION.trimmed.nt.nb', 'X3.D1.REGION.trimmed.nt.nb', 'X5.D2.REGION.trimmed.nt.nb', 'X3.D2.REGION.trimmed.nt.nb', 'X5.D3.REGION.trimmed.nt.nb', 'X3.D3.REGION.trimmed.nt.nb', 'D.REGION.nt.nb', 'D1.REGION.nt.nb', 'D2.REGION.nt.nb', 'D3.REGION.nt.nb') -out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")] +minimum_columns=c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele") +print_missing_columns(summ, minimum_columns) +out=summ[,minimum_columns] print(paste("nrow(summ)", nrow(summ))) print(paste("nrow(aa)", nrow(aa)))